Fig. 4

Characterization of myeloid cells and macrophage reprogramming upon ICI treatment. a Kaplan–Meier survival curve demonstrates the correlation of M1/M2 ratio with immunotherapy treatment outcomes in the bladder cancer (BLCA) cohort. b UMAP analysis delineates the clustering and subtypes of myeloid cells. c Bubble plot reveals the expression profiles of marker genes across myeloid cell subtypes. d Bar chart shows the proportional distribution of myeloid subtypes across four groups. e Pie chart shows the proportions of Spp1⁺ tumor-associated macrophages (TAMs), Cd74⁺ TAMs and cDC in normobiotic mice with their germ-free counterparts based on GSE181745 dataset. f Trajectory plot reveals the evolutionary paths and distinct states of macrophages/monocytes. g Bar graph shows the proportions of monocyte/macrophage subtypes across 7 evolutionary states. h Line graph reveals loess-regression-smoothened expression of the antigen-presenting (i.e., Cd74 and H2-Aa) and M2-related genes (i.e., Spp1 and Cxcl3) along pseudotime, the region in shade indicates the 95% confidence intervals. i Scatter plot shows the correlation of proportions of SPP1⁺ TAMs and CD74⁺ TAMs in two CRC cohorts with public scRNA-seq data. The left plot includes 50 tumor samples from the GSE178341 dataset, while the right plot includes 15 tumor samples from the GSE132465 dataset. j Representative spatial feature plots show the signature score of Immune cells, CD74⁺ TAMs and SPP1⁺ TAMs in tumor sections from a CRC patient sample (Qi et al.⁵¹). k Scatter plot reveals the correlation between signature scores of CD74⁺ TAMs and SPP1⁺ TAMs in immune cell-enriched region of the CRC tumor sample in (j). l Kaplan–Meier survival curves demonstrate the correlation of tumor-infiltrating CD74⁺ TAM/SPP1⁺ TAM proportion ratio with ICI treatment outcomes in two immunotherapy cohorts. m Box-and-whisker plots showing changes in the proportion of specific TAMs subtypes before and after treatment in the FMT cohort. The left panel represents the proportion of SPP1⁺ TAMs, the middle panel represents CD74⁺ TAMs, and the right panel shows the difference between CD74⁺ TAMs and SPP1⁺ TAMs. NR (non-responders) and R (responders) indicate different response groups to the treatment. The dataset includes a total of nine pairs of samples. n Bar plots illustrating the expression levels of macrophage-associated genes in M1 and M2 macrophages cultured under Akk-conditioned medium (Akk-CM) vs. control medium (Ctrl-Medium). The top row shows Cd74, Il6, and Inos expression in M1 macrophages, while the bottom row represents Cd163, Cd206, and Spp1 expression in M2 macrophages. Statistical significance is conducted with three replicates and indicated as *p < 0.05, **p < 0.01, and ***p < 0.001